# This file is the result of combining several RDB files, specifically # T0588.t04.dssp-ebghstl.rdb (weight 1.53986) # T0588.t04.stride-ebghtl.rdb (weight 1.24869) # T0588.t04.str2.rdb (weight 1.54758) # T0588.t04.alpha.rdb (weight 0.659012) # T0588.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0588.t2k.stride-ebghtl.rdb (weight 1.24869) # T0588.t2k.str2.rdb (weight 1.54758) # T0588.t2k.alpha.rdb (weight 0.659012) # These files were combined by translating their predictions into EHL # predictions with tables generated by compare-real, and then combining # those predictions with weights proportional to their mutual information # with the EHL alphabet. The comments from the individual files follow. # # Comments from T0588.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0588 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0588.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 455 # # ============================================ # Comments from T0588.t04.stride-ebghtl.rdb # ============================================ # TARGET T0588 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0588.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 455 # # ============================================ # Comments from T0588.t04.str2.rdb # ============================================ # TARGET T0588 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-str2-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0588.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 455 # # ============================================ # Comments from T0588.t04.alpha.rdb # ============================================ # TARGET T0588 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-alpha-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0588.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 455 # # ============================================ # Comments from T0588.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0588 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0588.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 132 # # ============================================ # Comments from T0588.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0588 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0588.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 132 # # ============================================ # Comments from T0588.t2k.str2.rdb # ============================================ # TARGET T0588 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0588.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 132 # # ============================================ # Comments from T0588.t2k.alpha.rdb # ============================================ # TARGET T0588 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0588.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 132 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0357 0.3165 0.6478 2 K 0.0493 0.7195 0.2312 3 N 0.0567 0.7806 0.1627 4 L 0.0440 0.8478 0.1082 5 L 0.0513 0.8110 0.1376 6 V 0.0426 0.7967 0.1608 7 C 0.0381 0.8063 0.1556 8 T 0.0325 0.8058 0.1617 9 L 0.0213 0.8126 0.1661 10 L 0.0163 0.8348 0.1489 11 F 0.0109 0.8815 0.1075 12 A 0.0080 0.9171 0.0749 13 Y 0.0079 0.9206 0.0715 14 A 0.0090 0.9205 0.0705 15 F 0.0104 0.9022 0.0873 16 T 0.0141 0.8538 0.1322 17 L 0.0325 0.6843 0.2832 18 N 0.0473 0.4283 0.5244 19 A 0.0846 0.2604 0.6550 20 Q 0.0771 0.1182 0.8047 21 V 0.0584 0.2078 0.7338 22 A 0.1157 0.1963 0.6880 23 N 0.3774 0.1567 0.4659 24 T 0.5968 0.0844 0.3188 25 R 0.4790 0.0621 0.4589 26 I 0.2268 0.0730 0.7002 27 Y 0.0148 0.7805 0.2047 28 A 0.0091 0.8501 0.1408 29 A 0.0071 0.9049 0.0881 30 E 0.0071 0.9256 0.0673 31 K 0.0071 0.9305 0.0624 32 L 0.0083 0.9308 0.0609 33 A 0.0080 0.9332 0.0588 34 K 0.0078 0.9355 0.0567 35 V 0.0071 0.9362 0.0568 36 K 0.0058 0.9305 0.0637 37 E 0.0068 0.9132 0.0800 38 K 0.0084 0.8607 0.1308 39 A 0.0357 0.5471 0.4172 40 D 0.0256 0.2115 0.7629 41 S 0.0451 0.1556 0.7993 42 P 0.0416 0.2581 0.7003 43 L 0.0436 0.3673 0.5892 44 Y 0.0257 0.5236 0.4507 45 A 0.0131 0.7834 0.2035 46 P 0.0088 0.8896 0.1017 47 A 0.0061 0.9276 0.0663 48 V 0.0052 0.9396 0.0551 49 K 0.0051 0.9436 0.0513 50 T 0.0049 0.9487 0.0464 51 L 0.0049 0.9472 0.0480 52 L 0.0050 0.9449 0.0501 53 R 0.0055 0.9333 0.0612 54 D 0.0073 0.9215 0.0712 55 A 0.0069 0.9200 0.0731 56 D 0.0061 0.9167 0.0773 57 K 0.0063 0.8941 0.0996 58 A 0.0099 0.8345 0.1557 59 L 0.0222 0.6699 0.3079 60 K 0.0272 0.3509 0.6218 61 M 0.0634 0.1321 0.8045 62 T 0.0591 0.0448 0.8961 63 P 0.1125 0.0725 0.8151 64 P 0.3107 0.0827 0.6066 65 S 0.4555 0.0704 0.4741 66 V 0.5797 0.0717 0.3486 67 M 0.6151 0.0613 0.3236 68 D 0.5195 0.0597 0.4207 69 K 0.3203 0.0689 0.6108 70 T 0.2193 0.0575 0.7232 71 M 0.1825 0.0486 0.7689 72 T 0.1841 0.0343 0.7817 73 A 0.1200 0.0503 0.8297 74 D 0.0910 0.0765 0.8325 75 S 0.0723 0.0857 0.8420 76 G 0.0611 0.0624 0.8766 77 D 0.0906 0.0631 0.8463 78 K 0.0584 0.3965 0.5451 79 H 0.0705 0.3917 0.5377 80 D 0.0930 0.4629 0.4441 81 Y 0.1410 0.3558 0.5031 82 M 0.1719 0.2505 0.5776 83 S 0.2104 0.1992 0.5905 84 M 0.1750 0.1993 0.6257 85 G 0.1476 0.0992 0.7532 86 P 0.1380 0.1173 0.7448 87 Y 0.1835 0.1384 0.6781 88 W 0.2357 0.1110 0.6533 89 W 0.1782 0.0592 0.7626 90 P 0.1521 0.0599 0.7880 91 D 0.1210 0.0530 0.8260 92 P 0.0426 0.1372 0.8202 93 S 0.0623 0.1212 0.8165 94 K 0.0820 0.0782 0.8397 95 P 0.0627 0.1513 0.7860 96 D 0.0633 0.1129 0.8237 97 G 0.0870 0.1036 0.8094 98 L 0.1612 0.0446 0.7942 99 P 0.2927 0.0413 0.6660 100 Y 0.5234 0.0402 0.4364 101 I 0.6430 0.0225 0.3345 102 R 0.3088 0.0310 0.6603 103 K 0.1086 0.0539 0.8375 104 D 0.0559 0.0605 0.8836 105 G 0.0924 0.0444 0.8632 106 Q 0.2679 0.0269 0.7052 107 R 0.5338 0.0253 0.4410 108 N 0.1615 0.0318 0.8067 109 P 0.0585 0.1958 0.7457 110 E 0.0369 0.2239 0.7393 111 L 0.0610 0.2109 0.7281 112 D 0.0600 0.1866 0.7534 113 K 0.0761 0.2529 0.6710 114 L 0.0526 0.3263 0.6212 115 D 0.0595 0.3702 0.5702 116 R 0.0154 0.8285 0.1562 117 N 0.0107 0.9018 0.0876 118 K 0.0095 0.9083 0.0822 119 L 0.0073 0.9304 0.0624 120 G 0.0063 0.9383 0.0555 121 D 0.0056 0.9317 0.0626 122 M 0.0052 0.9267 0.0681 123 S 0.0049 0.9422 0.0528 124 K 0.0049 0.9452 0.0499 125 A 0.0048 0.9466 0.0486 126 V 0.0047 0.9544 0.0409 127 T 0.0047 0.9584 0.0369 128 T 0.0047 0.9590 0.0363 129 L 0.0047 0.9587 0.0366 130 G 0.0047 0.9580 0.0373 131 L 0.0048 0.9557 0.0395 132 A 0.0048 0.9508 0.0444 133 Y 0.0063 0.9292 0.0645 134 Y 0.0144 0.8701 0.1155 135 F 0.0301 0.7181 0.2518 136 S 0.0554 0.3595 0.5851 137 G 0.0414 0.0734 0.8852 138 D 0.0559 0.1246 0.8195 139 E 0.0133 0.9133 0.0734 140 K 0.0077 0.9358 0.0565 141 Y 0.0061 0.9442 0.0497 142 A 0.0049 0.9587 0.0363 143 Q 0.0055 0.9569 0.0376 144 K 0.0048 0.9555 0.0397 145 A 0.0047 0.9578 0.0374 146 V 0.0047 0.9583 0.0369 147 D 0.0048 0.9562 0.0390 148 F 0.0050 0.9492 0.0458 149 L 0.0055 0.9478 0.0467 150 N 0.0057 0.9383 0.0560 151 V 0.0075 0.9175 0.0751 152 W 0.0141 0.8801 0.1059 153 F 0.0230 0.7710 0.2061 154 L 0.0357 0.5640 0.4003 155 D 0.0643 0.0913 0.8444 156 A 0.0276 0.3679 0.6045 157 K 0.0441 0.3973 0.5586 158 T 0.0670 0.4401 0.4930 159 K 0.1062 0.2846 0.6092 160 M 0.1588 0.1910 0.6503 161 N 0.0989 0.0788 0.8223 162 P 0.0369 0.1607 0.8024 163 H 0.0672 0.1169 0.8160 164 L 0.0929 0.1412 0.7658 165 T 0.1326 0.1803 0.6871 166 Y 0.1447 0.4095 0.4458 167 G 0.1881 0.4102 0.4017 168 Q 0.3017 0.3214 0.3769 169 T 0.3767 0.2002 0.4231 170 I 0.3225 0.1411 0.5364 171 P 0.2293 0.1568 0.6139 172 G 0.1524 0.1290 0.7185 173 K 0.1757 0.1357 0.6886 174 N 0.1588 0.1293 0.7119 175 K 0.1075 0.1620 0.7305 176 G 0.0936 0.1837 0.7227 177 M 0.1013 0.1834 0.7153 178 G 0.1319 0.1453 0.7229 179 R 0.1729 0.1369 0.6902 180 G 0.2852 0.1440 0.5708 181 A 0.3513 0.1599 0.4888 182 G 0.4327 0.1729 0.3944 183 M 0.3818 0.3606 0.2576 184 I 0.2976 0.4416 0.2608 185 D 0.1896 0.5085 0.3019 186 I 0.1018 0.6163 0.2819 187 Y 0.0527 0.6856 0.2617 188 S 0.0478 0.7359 0.2163 189 F 0.0348 0.8379 0.1273 190 T 0.0329 0.8609 0.1062 191 E 0.0320 0.8743 0.0937 192 M 0.0133 0.9298 0.0569 193 I 0.0085 0.9459 0.0456 194 D 0.0075 0.9494 0.0432 195 A 0.0059 0.9536 0.0405 196 M 0.0063 0.9532 0.0405 197 T 0.0055 0.9481 0.0465 198 L 0.0055 0.9295 0.0650 199 M 0.0086 0.8908 0.1005 200 E 0.0091 0.7912 0.1996 201 N 0.0177 0.5723 0.4101 202 S 0.0644 0.1544 0.7811 203 K 0.0287 0.1689 0.8024 204 A 0.0492 0.1303 0.8205 205 F 0.0736 0.0589 0.8676 206 T 0.0603 0.0475 0.8922 207 P 0.0058 0.9061 0.0881 208 K 0.0050 0.9294 0.0656 209 V 0.0053 0.9389 0.0558 210 K 0.0048 0.9541 0.0411 211 K 0.0048 0.9501 0.0452 212 G 0.0048 0.9444 0.0508 213 M 0.0047 0.9521 0.0431 214 K 0.0047 0.9578 0.0375 215 E 0.0048 0.9563 0.0389 216 W 0.0048 0.9533 0.0418 217 F 0.0048 0.9505 0.0447 218 T 0.0050 0.9461 0.0489 219 Q 0.0057 0.9268 0.0676 220 L 0.0068 0.9021 0.0912 221 V 0.0126 0.8853 0.1021 222 E 0.0175 0.8623 0.1202 223 W 0.0232 0.8508 0.1260 224 M 0.0404 0.8187 0.1408 225 Q 0.0616 0.7177 0.2207 226 T 0.0657 0.4905 0.4438 227 S 0.0657 0.2136 0.7208 228 P 0.0266 0.2588 0.7146 229 V 0.0372 0.2490 0.7138 230 A 0.0437 0.2679 0.6884 231 A 0.0341 0.5925 0.3734 232 E 0.0330 0.6916 0.2754 233 E 0.0265 0.7737 0.1998 234 Q 0.0369 0.7506 0.2125 235 R 0.0395 0.6964 0.2641 236 A 0.0400 0.6240 0.3360 237 K 0.0310 0.4750 0.4940 238 N 0.0417 0.3409 0.6174 239 N 0.0359 0.4222 0.5419 240 H 0.0268 0.6359 0.3373 241 G 0.0147 0.8162 0.1691 242 L 0.0074 0.9058 0.0868 243 A 0.0054 0.9441 0.0504 244 Y 0.0047 0.9564 0.0389 245 D 0.0047 0.9582 0.0371 246 V 0.0047 0.9596 0.0357 247 Q 0.0047 0.9599 0.0354 248 L 0.0047 0.9598 0.0355 249 T 0.0047 0.9600 0.0353 250 A 0.0047 0.9602 0.0351 251 Y 0.0047 0.9599 0.0354 252 A 0.0050 0.9549 0.0402 253 L 0.0056 0.9410 0.0534 254 Y 0.0106 0.8527 0.1367 255 T 0.0484 0.5311 0.4205 256 G 0.0371 0.0918 0.8711 257 N 0.0774 0.1164 0.8062 258 Q 0.0072 0.9159 0.0769 259 D 0.0056 0.9398 0.0546 260 L 0.0050 0.9493 0.0457 261 A 0.0047 0.9558 0.0394 262 M 0.0047 0.9554 0.0399 263 K 0.0048 0.9531 0.0421 264 T 0.0048 0.9508 0.0444 265 I 0.0048 0.9456 0.0496 266 Q 0.0051 0.9268 0.0682 267 E 0.0060 0.8916 0.1024 268 F 0.0102 0.8374 0.1524 269 P 0.0101 0.7916 0.1983 270 E 0.0142 0.7721 0.2138 271 K 0.0259 0.6540 0.3201 272 R 0.0468 0.6127 0.3405 273 L 0.0549 0.5567 0.3884 274 F 0.0341 0.6824 0.2835 275 A 0.0459 0.6331 0.3210 276 Q 0.0972 0.5155 0.3873 277 I 0.2250 0.2674 0.5076 278 E 0.1036 0.1318 0.7647 279 P 0.0351 0.1786 0.7863 280 D 0.0474 0.0690 0.8836 281 G 0.0479 0.0568 0.8953 282 K 0.1169 0.0624 0.8207 283 Q 0.1423 0.0653 0.7924 284 P 0.1186 0.1896 0.6918 285 L 0.0979 0.4635 0.4385 286 E 0.1400 0.4931 0.3670 287 L 0.1691 0.4562 0.3747 288 A 0.2052 0.3546 0.4402 289 R 0.2158 0.2666 0.5176 290 T 0.1443 0.2151 0.6406 291 T 0.1039 0.1599 0.7362 292 A 0.0746 0.3661 0.5593 293 L 0.0739 0.5130 0.4131 294 G 0.1265 0.5934 0.2801 295 Y 0.2040 0.5656 0.2304 296 T 0.1872 0.6291 0.1837 297 I 0.1622 0.6709 0.1670 298 F 0.1187 0.6126 0.2687 299 N 0.0797 0.5752 0.3451 300 L 0.0080 0.8841 0.1079 301 G 0.0051 0.9387 0.0561 302 H 0.0047 0.9503 0.0450 303 M 0.0047 0.9566 0.0387 304 L 0.0047 0.9585 0.0368 305 D 0.0047 0.9594 0.0359 306 M 0.0047 0.9588 0.0365 307 C 0.0047 0.9575 0.0378 308 S 0.0048 0.9551 0.0401 309 I 0.0048 0.9456 0.0496 310 A 0.0053 0.9255 0.0692 311 S 0.0060 0.8820 0.1120 312 T 0.0093 0.7839 0.2069 313 L 0.0434 0.4413 0.5153 314 G 0.0496 0.0990 0.8513 315 Q 0.0933 0.1070 0.7997 316 D 0.2359 0.1257 0.6384 317 I 0.1278 0.4602 0.4120 318 Y 0.1569 0.4622 0.3808 319 N 0.2401 0.3971 0.3628 320 A 0.2941 0.2695 0.4364 321 T 0.3668 0.1279 0.5053 322 S 0.1199 0.0749 0.8052 323 Q 0.0182 0.1885 0.7932 324 D 0.0414 0.0872 0.8715 325 G 0.0310 0.1706 0.7984 326 R 0.0883 0.4098 0.5020 327 S 0.1910 0.5395 0.2694 328 I 0.0115 0.9318 0.0567 329 T 0.0096 0.9399 0.0505 330 A 0.0079 0.9404 0.0517 331 A 0.0074 0.9441 0.0485 332 L 0.0066 0.9465 0.0469 333 K 0.0064 0.9260 0.0676 334 F 0.0071 0.8779 0.1150 335 L 0.0265 0.8095 0.1640 336 I 0.0296 0.7382 0.2322 337 P 0.0193 0.6838 0.2969 338 Y 0.0291 0.5921 0.3788 339 I 0.0694 0.3985 0.5321 340 G 0.0445 0.2501 0.7054 341 K 0.0494 0.1228 0.8279 342 P 0.0579 0.1608 0.7813 343 Q 0.1166 0.1637 0.7197 344 S 0.1280 0.1431 0.7289 345 E 0.1152 0.1057 0.7791 346 W 0.1080 0.1455 0.7465 347 P 0.1141 0.2214 0.6645 348 Y 0.1186 0.2313 0.6501 349 Q 0.1283 0.2138 0.6579 350 Q 0.1128 0.2025 0.6847 351 I 0.1101 0.1877 0.7022 352 K 0.0980 0.2564 0.6457 353 E 0.1043 0.2851 0.6106 354 W 0.0871 0.3226 0.5904 355 D 0.0489 0.4860 0.4651 356 K 0.0402 0.5439 0.4160 357 K 0.0429 0.5919 0.3652 358 Q 0.0518 0.5581 0.3901 359 E 0.0500 0.5745 0.3755 360 E 0.0397 0.6056 0.3546 361 A 0.0376 0.6004 0.3620 362 C 0.0236 0.6915 0.2849 363 W 0.0195 0.6989 0.2817 364 I 0.0201 0.7499 0.2301 365 L 0.0132 0.7852 0.2017 366 R 0.0179 0.7218 0.2604 367 R 0.0295 0.6479 0.3226 368 A 0.0472 0.4911 0.4617 369 S 0.0444 0.3129 0.6428 370 F 0.0584 0.2500 0.6917 371 F 0.0654 0.2519 0.6827 372 D 0.0584 0.2074 0.7341 373 P 0.0300 0.5511 0.4189 374 K 0.0151 0.7328 0.2521 375 A 0.0170 0.7770 0.2060 376 G 0.0118 0.8475 0.1407 377 Y 0.0141 0.8736 0.1123 378 E 0.0168 0.9045 0.0786 379 A 0.0198 0.9088 0.0713 380 I 0.0220 0.9059 0.0721 381 G 0.0186 0.9036 0.0778 382 A 0.0181 0.8729 0.1090 383 Q 0.0203 0.7995 0.1803 384 F 0.0357 0.6163 0.3479 385 R 0.0358 0.3431 0.6212 386 E 0.0503 0.1628 0.7868 387 T 0.0626 0.0882 0.8491 388 P 0.0201 0.4055 0.5744 389 A 0.0384 0.4613 0.5003 390 N 0.0273 0.7230 0.2497 391 K 0.0262 0.8225 0.1513 392 R 0.0255 0.8688 0.1057 393 I 0.0198 0.8849 0.0953 394 H 0.0190 0.8692 0.1118 395 L 0.0242 0.7848 0.1910 396 I 0.0276 0.6647 0.3077 397 Y 0.0683 0.3376 0.5941 398 S 0.0649 0.1000 0.8352 399 L 0.0372 0.1158 0.8470 400 E 0.0271 0.0630 0.9099